Contacts of the helix formed by residues 430 - 445 (chain L) in PDB entry 1I43
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 430 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I SER* 2.7 41.8 + - - +
58I GLY* 4.5 7.5 - - - -
59I SER* 2.9 14.1 + - - +
311I HIS* 4.9 6.9 + - - +
315I GLN* 5.4 5.2 + - - -
316L GLN* 4.5 5.6 + - - +
429L GLU* 1.3 71.6 - - - +
431L PHE* 1.3 68.2 + - - +
432L ASP* 4.5 13.7 + - - +
433L ASP* 3.0 19.1 + - - +
434L LEU* 3.0 10.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 431 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316L GLN* 4.6 4.5 - - - +
320L THR* 3.9 27.4 - - + +
323L ARG* 3.0 61.5 - - + +
324L MET* 3.5 31.9 - - + -
327L ILE* 3.9 24.5 - - + -
429L GLU 3.3 5.1 + - - -
430L ASP* 1.3 72.3 + - - +
432L ASP* 1.3 67.4 + - - +
434L LEU* 2.8 9.0 + - - +
435L LYS* 2.6 51.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 432 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I SER* 6.4 0.2 - - - -
430L ASP* 3.3 12.5 + - + +
431L PHE* 1.3 90.7 - - - +
433L ASP* 1.3 65.8 + - - +
435L LYS* 3.9 15.5 + - - +
436L ALA* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 433 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I PHE 3.8 9.2 - - - +
55I ASN* 3.2 35.4 + - - +
56I SER* 3.1 29.2 + - - -
59I SER* 2.7 29.0 + - - +
382L ILE* 3.3 23.6 - - + +
429L GLU* 5.3 0.9 - - + -
430L ASP 3.0 10.1 + - - +
432L ASP* 1.3 79.5 - - - +
434L LEU* 1.3 62.7 + - - +
436L ALA* 3.9 4.3 - - - +
437L ASP* 3.2 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 434 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320L THR* 3.7 28.9 - - + -
324L MET* 5.5 0.4 - - + -
382L ILE* 4.1 19.3 - - + -
383L PRO* 5.4 0.9 - - + -
394L SER* 3.4 28.3 - - - +
424L PHE* 4.5 9.4 - - + -
426L PHE* 4.3 16.6 - - + -
427L GLY 4.8 4.3 - - - +
429L GLU* 3.6 40.6 - - + +
430L ASP 3.0 9.1 + - - +
431L PHE* 2.8 7.8 + - + +
433L ASP* 1.3 75.5 - - - +
435L LYS* 1.3 66.4 + - - +
437L ASP* 2.9 14.8 + - + +
438L ILE* 3.0 19.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 435 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324L MET* 3.7 26.6 - - - -
327L ILE* 3.9 24.3 - - + +
431L PHE* 2.6 35.8 + - + +
432L ASP* 3.9 14.4 + - - +
434L LEU* 1.3 73.4 - - - +
436L ALA* 1.3 67.2 + - - +
438L ILE* 3.2 2.0 + - - +
439L LEU* 2.9 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 436 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432L ASP 3.0 19.5 + - - +
433L ASP* 3.9 5.2 - - - +
435L LYS* 1.3 80.6 - - - +
437L ASP* 1.3 57.3 + - - +
439L LEU* 3.8 6.8 - - - +
440L GLN* 2.8 33.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 437 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I PHE* 5.4 4.8 - - + +
380L LEU* 3.8 8.5 - - - +
381L LYS* 3.2 35.3 + - - +
382L ILE* 3.2 24.2 + - + +
383L PRO* 3.3 13.5 - - - +
424L PHE* 5.7 0.2 - - - -
433L ASP 3.2 11.8 + - - +
434L LEU* 2.9 11.8 + - + +
436L ALA* 1.3 78.9 - - - +
438L ILE* 1.3 65.5 + - + +
440L GLN* 2.9 26.0 - - - +
441L ALA* 2.8 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 438 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324L MET* 3.4 23.8 - - + -
328L LEU* 4.0 27.4 - - + -
364L PHE* 5.5 0.9 - - + -
376L PHE* 3.7 12.1 - - + -
380L LEU* 3.9 11.0 - - + -
424L PHE* 3.9 26.0 - - + -
426L PHE* 3.4 37.2 - - + -
434L LEU* 3.0 15.2 + - + +
435L LYS 3.7 5.4 - - - +
437L ASP* 1.3 77.6 - - + +
439L LEU* 1.3 64.8 + - + +
441L ALA* 3.3 2.8 + - - +
442L LEU* 3.0 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 439 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324L MET* 5.7 1.8 - - + -
327L ILE* 4.3 19.7 - - + -
328L LEU* 6.2 0.7 - - + -
331L HIS* 4.0 26.9 + - + +
435L LYS* 2.9 47.7 + - + +
436L ALA* 3.8 6.1 - - - +
438L ILE* 1.3 77.0 - - + +
440L GLN* 1.3 67.6 + - - +
442L LEU* 3.0 20.9 + - + +
443L ASP* 3.1 17.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 440 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379L ALA* 3.4 24.4 + - - +
381L LYS* 4.1 22.5 + - - +
436L ALA 2.8 20.2 + - - +
437L ASP* 2.9 33.5 - - - +
439L LEU* 1.3 71.4 - - - +
441L ALA* 1.3 73.9 + - - +
443L ASP* 3.2 26.1 + - - +
444L SER* 3.6 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 441 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376L PHE* 3.5 31.8 - - + +
379L ALA* 3.9 13.1 - - + +
380L LEU* 3.6 17.3 - - + +
437L ASP 2.8 13.0 + - - +
438L ILE 3.4 8.7 - - - +
440L GLN* 1.3 85.8 - - - +
442L LEU* 1.3 63.5 + - - +
444L SER* 2.9 22.3 + - - -
445L ILE* 3.9 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 442 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328L LEU* 4.1 11.0 - - + -
331L HIS* 3.5 37.9 - - + +
333L LYS* 3.4 29.1 + - + +
334L VAL* 4.3 12.6 - - + -
364L PHE* 5.7 0.4 - - + -
366L VAL* 5.2 4.3 - - + -
376L PHE* 3.7 19.3 - - + -
438L ILE* 3.0 32.2 + - + +
439L LEU* 3.0 14.2 + - + +
441L ALA* 1.3 75.7 - - - +
443L ASP* 1.3 63.2 + - - +
445L ILE* 3.3 39.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 443 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331L HIS* 5.3 5.0 + - - -
333L LYS* 3.6 17.0 + - - +
439L LEU* 3.1 17.8 + - - +
440L GLN* 3.3 15.9 - - - +
441L ALA 3.0 0.4 + - - -
442L LEU* 1.3 79.7 - - - +
444L SER* 1.3 62.8 + - - +
445L ILE 3.0 2.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 444 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375L LYS* 4.4 23.6 - - - +
376L PHE* 6.2 0.2 - - - -
379L ALA* 4.0 16.8 - - - +
440L GLN* 3.6 10.6 + - - -
441L ALA* 2.9 15.0 + - - -
443L ASP* 1.3 76.4 - - - +
445L ILE* 1.3 62.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 445 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333L LYS* 4.1 29.6 - - + -
366L VAL* 3.8 22.2 - - + -
367L ASP 5.0 6.5 - - - +
372L THR* 3.9 26.0 - - + +
375L LYS* 4.8 10.4 - - + +
376L PHE* 3.7 34.8 - - + +
441L ALA 4.4 2.2 - - - +
442L LEU* 3.3 34.5 - - + +
443L ASP 3.0 7.5 + - - -
444L SER* 1.3 84.6 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il